/usr/share/pyshared/Epigrass/manager.py is in epigrass 2.0.4-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""
Model Management and simulation objects.
"""
import cPickle, time
import os, codecs, subprocess
from copy import deepcopy
from xmlrpclib import ServerProxy, Error
from simobj import graph, edge, siteobj
from numpy import *
import spread
from numpy.random import uniform, poisson
from sqlobject import *
from math import *
from data_io import *
from optparse import OptionParser
import ConfigParser
import string, sys, getpass
import report as Rp
import epigdal
import __version__
import encodings.utf_8
import encodings.latin_1
import dataObject as DO
import MySQLdb
from pysqlite2 import dbapi2 as sqlite3
#import pycallgraph
# Import Psyco if available
#try:
# import psyco
#
# psyco.full()
#except ImportError:
# pass
class simulate:
"""
This class takes care of setting up the model, simulating it, and storing the results
"""
def __init__(self, fname=None, host='localhost',port=3306,db='epigrass',user='epigrass', password='epigrass',backend = 'mysql'):
#pycallgraph.start_trace()
self.host = host
self.port = port
self.usr = user
self.db = db
self.fname = fname
self.backend = backend
self.passw = password
self.repname = None
self.shapefile = None
self.World = None
self.shpout = True
self.dir = os.getcwd()
sys.path.insert(0,self.dir) #add current path to sys.path
self.gui = 0 # True if this object was created by the gui
self.now = time.asctime().replace(' ','_').replace(':','') #current date and time
self.modelName = os.path.split(self.fname)[-1].split('.')[0]
self.config = self.loadModelScript(self.fname)
self.evalConfig(self.config)
if not self.outdir:
self.outdir = outdir = 'outdata-'+self.modelName
if not os.path.exists(self.outdir):
os.mkdir(self.outdir)
if self.shapefile: #create world object if a shapefile is provided
self.World = epigdal.World(*self.shapefile+[self.outdir])
self.chkScript()
self.encoding = 'latin-1'#default encoding for strings in the sites and edges files
self.round = 0 #No replicates
sitios = loadData(self.sites, sep=',', encoding=self.encoding)
ed = loadData(self.edges,sep=',', encoding=self.encoding)
l = self.instSites(sitios)
e = self.instEdges(l,ed)
self.g = self.instGraph(self.modelName,1,l,e)
#if self.layer:
# pass
#self.grassVect2ascii(self.layer)
#self.g.plotDegreeDist()
def loadModelScript(self,fname):
"""
Loads the model specification from the text file.
Returns a dictionary with keys of the form
<section>.<option> and the corresponding values.
"""
config = {}
config = config.copy()
cp =ConfigParser.SafeConfigParser()
cp.read(fname)
for sec in cp.sections():
name = string.lower(sec)
for opt in cp.options(sec):
config[name+"."+string.lower(opt)] = string.strip(cp.get(sec,opt))
return config
def evalConfig(self,config):
"""
Takes in the config dictionary and generates the global variables needed.
"""
try:
#WORLD
#load Shapefile if specified
if config['the world.shapefile']:
self.shapefile = eval(config['the world.shapefile'])
else:
self.shapefile = []
#self.layer = config['the world.vector layer']
self.sites = config['the world.sites'] #file containing site info
self.edges = config['the world.edges'] #file containing edge info
if config['the world.encoding']:
self.encoding = config['the world.encoding']#encoding specification
#Epidemiological model
self.modtype = config['epidemiological model.modtype']
#self.models = eval(config['epidemiological model.models'])
#PARAMETERS
self.beta = config['model parameters.beta']
self.alpha = config['model parameters.alpha']
self.e = config['model parameters.e']
self.r = config['model parameters.r']
self.delta = config['model parameters.delta']
self.B = config['model parameters.b']
self.w = config['model parameters.w']
self.p = config['model parameters.p']
#INITIAL CONDITIONS (inits are string to evaluated inside siteobj.createmodel)
self.S = config['initial conditions.s']
self.E = config['initial conditions.e']
self.I = config['initial conditions.i']
#EPIDEMIC EVENTS
self.seed = eval(config['epidemic events.seed'])
self.vaccinate = eval(config['epidemic events.vaccinate'])
#self.quarantine = eval(config['epidemic events.quarantine'])
#[TRANSPORTATION MODEL]
self.doTransp = eval(config['transportation model.dotransp'])
self.stochTransp = eval(config['transportation model.stochastic'])
self.speed = eval(config['transportation model.speed'])
#SIMULATION AND OUTPUT
self.steps = eval(config['simulation and output.steps'])
self.outdir = config['simulation and output.outdir']
self.MySQLout = eval(config['simulation and output.mysqlout'])
# self.Rep = eval(config['simulation and output.report'])
# self.siteRep = eval(config['simulation and output.siterep'])
self.replicas = eval(config['simulation and output.replicas'])
self.randomize_seeds = eval(config['simulation and output.randseed'])
self.Batch = eval(config['simulation and output.batch'])
except KeyError, v:
V = v.__str__().split('.')
sys.exit("Please check the syntax of your '.epg' file.\nVariable %s, from section %s was not specified."%(V[1],V[0]))
if self.replicas:
# self.Rep = 0 #Turns off reports
self.Batch = []#Turns off Batch mode
self.round = 0# Initialize replicate counter
# generate dictionaries for parameters and inits
self.inits = {}
self.parms = {}
for k,v in config.items():
if k.startswith('initial conditions'):
self.inits[k.split('.')[-1]] = v
elif k.startswith('model parameters'):
self.parms[k.split('.')[-1]] = v
else:pass
def chkScript(self):
"""
Checks the type of the variables on the script
"""
self.Say("Checking syntax of model script... NOW")
if not os.access(self.sites,os.F_OK):
self.Say('Sites file %s does not exist, please check your script.'%self.sites)
sys.exit()
if not os.access(self.edges,os.F_OK):
self.Say('Egdes file %s does not exist, please check your script.'%self.edges)
sys.exit()
if not self.modtype in ['SIS','SIS_s','SIR','SIR_s','SEIS','SEIS_s','SEIR','SEIR_s','SIpRpS','SIpRpS_s','SIpR,SIpR_s','Influenza','Custom']:
self.Say('Model type %s is invalid, please check your script.'%self.modtype)
self.Say('Script %s passed syntax check NOW.'%self.modelName)
def deg2dec(self,coord):
"""
converts lat/long to decimal
"""
co = coord.split(':')
if int(co[0])<0:
result = float(co[0])-float(co[1])/60-float(co[2])/3600
else:
result = float(co[0])+float(co[1])/60+float(co[2])/3600
return result
def instSites(self,sitelist):
"""
Instantiates and returns a list of siteobj instances, from a list of site specification
as returned by data_io.loadData.
Here the site specific events are passed to each site, and the site models are created.
"""
header = sitelist.pop(0)
objlist=[]
for site in sitelist:
if ':' in site[0]:
lat = self.deg2dec(site[0])
long = self.deg2dec(site[1])
else:
lat = float(site[0])
long = float(site[1])
objlist.append(siteobj(site[2],site[3],(lat,long),int(strip(site[4])),tuple([float(strip(i)) for i in site[5:]])))
for o in objlist:
if self.stochTransp: o.stochtransp = 1
N = o.totpop #local copy for reference on model creation
values = o.values #local copy for reference on model creation
inits={}
parms={}
#eval parms and inits
for k,v in self.inits.items():
inits[k] = eval(v)
for k,v in self.parms.items():
parms[k] = eval(v)
#Linhas abaixo estao obsoletas (remover quando tiver tempo para testar)
I = eval(self.I)
E = eval(self.E)
S = eval(self.S)
beta = eval(self.beta)
alpha = eval(self.alpha)
e = eval(self.e)
r = eval(self.r)
delta = eval(self.delta)
B = eval(self.B)
w = eval(self.w)
p = eval(self.p)
#################
if self.vaccinate:
if self.vaccinate[0][0] == 'all':
o.vaccination = [self.vaccinate[0][1],self.vaccinate[0][2]]
else:
for i in self.vaccinate:
if int(o.geocode) == i[0]:
o.vaccination = [i[1],float(i[2])]
# if self.quarantine:
# for i in self.quarantine:
# if int(o.geocode) == i[0]:
# o.quarantine == i[1:]
if self.seed:
#print type(o.geocode), type(self.seed[0])
if self.seed[0][0] == "all":
I += j[2]
inits[self.seed[0][1].lower()] += 1
for j in self.seed:
if int(o.geocode) == j[0]:
#self.Say("%s infected person(s) arrived at %s"%(j[2],o.sitename))
I += j[2]
inits[j[1].lower()] +=j[2]
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
else:
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
else:
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
return objlist
def instEdges(self,sitelist, edgelist):
"""
Instantiates and returns a list of edge objects,
sitelist -- list of siteobj objects.
edgelist -- list of edge specifications as returned by data_io.loadData.
"""
header = edgelist.pop(0)
#print [i.sitename for i in sitelist]
objlist=[]
source = dest = None
for edg in edgelist:
#print edgelist.index(edg)
if edg[5] == edg[6]:
#ignore circular edges
continue
for site in sitelist:
#print site.sitename
if str(site.geocode) == edg[5]:
source = site
#print 'found source = ',source.sitename
elif str(site.geocode) == edg[6]:
dest = site
#print 'found dest = ',dest.sitename
if (source and dest):
#print 'next edge!'
break
if not (source and dest):
#print source ,dest
sys.exit('One of the vertices on edge '+edg[0]+'-'+edg[1]+' could not be found on the site list')
objlist.append(edge(source,dest,edg[2],edg[3],float(edg[4])))
source = dest = None
return objlist
def instGraph(self,name, digraph, siteobjlist, edgeobjlist):
"""
Instantiates and returns a graph object from a list of edge objects.
"""
g = graph(name,digraph)
g.speed = self.speed
for j in siteobjlist:
g.addSite(j)
for i in edgeobjlist:
g.addEdge(i)
return g
def randomizeSeed(self, option):
"""
Generate and return a list of randomized seed sites
to be used in a repeated runs scenario.
Seed sites are sampled with a probability proportional to the
log of their population size.
option: if 1 randomize; if 2, return unrundomized sequence
"""
if option==1:
poplist = [log10(site.totpop) for site in self.g.site_list]
lpl = len(poplist)
popprob = array(poplist)/sum(poplist) #acceptance probability
u = floor(uniform(0,lpl, self.replicas))
sites=[]
i=0
while i < self.replicas:
p = uniform(0,1)
if p <= popprob[int(u[i])]:
sites.append(self.g.site_list[int(u[i])])
i += 1
elif option ==2:
sites = self.g.site_list
return sites
def setSeed(self,seed,n=1):
'''
Resets the number of infected to zero in all nodes but seed,
which get n infected cases.
seed must be a siteobj object.
'''
#inits[self.seed[0][1].lower()] += 1
seedvar = self.seed[0][1].lower() #retrieve the name of the variable containing the seeds
self.Say('seedvar= %s'%seedvar)
self.seed =[(seed.geocode, seedvar,n)]
for site in self.g.site_list:
if site.geocode == seed.geocode:
site.bi[seedvar] = n
# site.ts[0][seedpos] = n
self.Say("%s infected case(s) arrived at %s"%(n,seed.sitename))
else:
site.bi[seedvar] = 0
# site.ts[0][seedpos] = 0
def start(self):
"""
Start the simulation
"""
if '/' in self.modelName:
self.modelName = os.path.split(self.modelName)[-1]
# print "====>", self.gui
# if self.gui and not self.round: #open the display window only on the first round of a reprun
# subprocess.Popen(['python','Epigrass/dgraph.py'])
# self.dserver = ServerProxy("http://localhost:50000", allow_none = True) # local display server
time.sleep(10)
self.Say('Simulation starting.')
start = time.time()
self.runGraph(self.g,self.steps,transp=self.doTransp)
elapsed = time.time()-start
self.Say('Simulation lasted %s seconds.'%elapsed)
if self.MySQLout:
if self.backend == 'csv':
self.outToCsv(self.modelName)
else:
self.outToDb(self.modelName)
if self.shpout:
self.outToShp()
self.dumpData()
spread.Spread(self.g, self.outdir, self.encoding)
#self.saveModel(self.modelName)
#pycallgraph.make_dot_graph(self.modelName+'_callgraph.png')
#print len(self.g.site_list[-1].ts)
## for i in self.g.site_list:
## i.plotItself()
## show()
def createDataFrame(self,site):
"""
Saves the time series *site.ts* to outfile as specified on the
model script.
"""
data = array(site.ts, Float)
inc = site.incidence
f = open(self.outdir+self.outfile,'w')
f.write('time,E,I,S,incidence\n')
try:
for t,i in enumerate(data):
j = [str(k) for k in i]
line = str(t)+','.join(j) + str(inc[t])+'\n'
f.write(line)
finally:
f.close()
return 'E,I,S\n'+tss
def grassVect2ascii(self,layer):
"""
Convert Grass vector layer to an ascii file epigrass can read
Deprecated!
"""
com = 'v.out.ascii input=%s output=map.txt format=standard'%layer
os.system(com)
def outToShp(self):
"""
Creates Data Layers in shapefile format
"""
if not self.World:
return
#Initialize world output layers
self.Say("REading Nodes from shapefile...")
self.World.getNodeList(self.World.ds.GetLayerByName(self.World.layerlist[0]))
self.Say("Done reading nodes!")
self.Say("Creating Nodes shapefile...")
self.World.createNodeLayer()
self.Say("Done creating Nodes shapefile!")
elist = [(e.source.geocode,e.dest.geocode,sum(e.ftheta),sum(e.btheta)) for e in self.g.edge_list]
self.Say("Creating Edges shapefile...")
self.World.createEdgeLayer(elist)
self.Say("Done creating Edges shapefile!")
#Generate site epidemic stats
varlist = ["prevalence","totalcases", "arrivals","population"]
sitestats = []
names = {}
for site in self.g.site_list:
names[int(site.geocode)] = site.sitename
prevalence = float(site.totalcases)/site.totpop
#print prevalence
sitestats.append((site.geocode,prevalence,site.totalcases,sum(site.thetahist),float(site.totpop)))
self.Say("Creating Data shapefile...")
self.World.createDataLayer(varlist,sitestats)
self.Say("Done creating Data shapefile!")
#Generate the kml too.
self.Say("Creating KML output file...")
lr = self.World.datasource.GetLayer(0)
k = epigdal.KmlGenerator()
k.addNodes(lr,names)
k.writeToFile(self.outdir)
self.Say("Done creating KML file!")
#close files
self.World.closeSources()
def writeMetaCSV(self, table):
"""
Writes a meta CSV table
"""
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
f = open(table+'_meta', 'w')
cfgitems = self.config.items()
h = ';'.join([k.strip().replace(' ','_').replace('.', '$') for k,v in cfgitems])
l = ';'.join([v.split('#')[0] for k, v in cfgitems])
f.write(h+'\n')
f.write(l+'\n')
f.close()
os.chdir(self.dir)
def outToCsv(self,table):
"""
Save simulation results in csv file.
"""
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
tablee = table+"_"+self.now+"_e.tab" #edgetable name
table += "_"+self.now+".tab"#sitetable name
f = open(table,"w")
head = ['geocode','time','totpop','name',
'lat','longit']
headerwritten = False
for site in self.g.site_list:
t = 0
regb = [str(site.geocode),str(t),str(site.totpop),
site.sitename.replace('"','').encode('ascii','replace'),
str(site.pos[0]),str(site.pos[1])
]
if site.values:
for n,v in enumerate(site.values):
head.append('values%s'%n)
regb.append(str(v))
#print site.sitename, site.ts
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
head.extend(['incidence','arrivals'])
for n,v in enumerate(site.vnames):
head.append(str(v))
for i in ts:
reg = deepcopy(regb)
reg.extend([str(site.incidence[t]),str(site.thetahist[t])])
reg[1] = str(t)
for n,v in enumerate(site.vnames):
reg.append(str(i[n]))
if not headerwritten:
h =",".join(head)
f.write(h+'\n')
headerwritten = True
f.write(','.join(reg)+'\n')
t += 1
f.close()
#inserting data in edges file
g = open(tablee,'w')
t=0
head = ['source_code','dest_code','time','ftheta','btheta']
ehw = False
for e in self.g.edge_list:
for f,b in zip(e.ftheta,e.btheta):
if not ehw:
g.write(','.join(head)+'\n')
ehw = True
ereg = [e.source.geocode,e.dest.geocode,t,f,b]
ereg = [str(i) for i in ereg]
g.write(','.join(ereg)+'\n')
t += 1
g.close()
os.chdir(self.dir)
def outToODb(self,table,mode='b'):
"""
Insert simulation results in a database using sqlobject.
if mode = b, do batch inserts
if mode = p, do parallel inserts
"""
#set connection parameters
try:
DO.Connect(self.backend.lower(),self.usr,self.passw,self.host,self.port,self.db)
self.Say('Saving data on %s database...'%self.backend)
except:
self.Say('Database Connection Failed')
#basic connection variables
name = table+'_'+self.now
self.outtable = name
DO.Site.sqlmeta.table = name
DO.Edge.sqlmeta.table = name+'e'
if self.backend.lower()=='sqlite':
DO.Site.sqlmeta.createSQL = {'sqlite':['PRAGMA synchronous=OFF;','PRAGMA default_cache_size=12000000;']}
DO.Site._connection.commit()
DO.Edge.sqlmeta.createSQL = {'sqlite':['PRAGMA synchronous=OFF;','PRAGMA default_cache_size=12000000;']}
DO.Edge._connection.commit()
#adding columns to sites table
try: #Only add if they don't exist. On Batch runs this will catch the add error
DO.Site.sqlmeta.addColumn(StringCol('incidence'))
DO.Site.sqlmeta.addColumn(StringCol('arrivals'))
except: pass
if self.g.site_list[0].values:#add columns for 'values' variables
for i in xrange(len(self.g.site_list[0].values)):
try:
DO.Site.sqlmeta.addColumn(StringCol('values%s'%i))
except: pass
for s in self.g.site_list[0].vnames: #add columns for state variables
try:
DO.Site.sqlmeta.addColumn(StringCol(s))
except: pass
#creating tables
DO.Site.createTable()
DO.Edge.createTable()
#saving pickle of adjacency matrix
matname = 'adj_'+self.modelName # table
adjfile = open(matname,'w')
cPickle.dump(self.g.getConnMatrix(),adjfile)
adjfile.close()
#calling insert function
if mode == 'b':
self.batchInsert()
elif mode == 'p':
self.parInsert()
def batchInsert(self):
"""
Do the inserts all at once. After the simulation is done
"""
#inserting data in sites table
for site in self.g.site_list:
dicin={
'geocode':site.geocode,
'lat':float(site.pos[0]),
'longit':float(site.pos[1]),
'name':site.sitename.replace('"','').encode('ascii','replace'),
'totpop':int(site.totpop)}
if site.values:
for n,v in enumerate(site.values):
#print v,type(v)
dicin['values%s'%n] = str(v)
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
t = 0
for i in ts:
dicin['incidence']= str(site.incidence[t])
dicin['arrivals'] = str(site.thetahist[t])
dicin['time'] = t
for n,v in enumerate(site.vnames):
#print i[n],type( i[n])
dicin[v] = str(i[n])
DO.Site(**dicin)
t += 1
#DO.Site._connection.commit()
#inserting data in edges table
for e in self.g.edge_list:
rlist = []
edicin={
'source_code':e.source.geocode,
'dest_code':e.dest.geocode}
t=0
for f,b in zip(e.ftheta,e.btheta):
edicin['time'] = t
edicin['ftheta'] = f
edicin['btheta'] = b
rlist.append(edicin)
t += 1
insobj = DO.sqlbuilder.Insert(DO.Edge.sqlmeta.table,valueList=rlist)
DO.Edge._connection.queryAll(DO.Edge._connection.sqlrepr(insobj))
#DO.Edge._connection.commit()
def parInsert(self):
"""
do the insertions in a separate process.
"""
pid = os.fork()
if pid:
#parent process get on with the simulation
return
else:
#child process inserts data in sites table
time.sleep(1+self.g.simstep)
for site in self.g.site_list:
dicin={
'geocode':site.geocode,
'lat':float(site.pos[0]),
'longit':float(site.pos[1]),
'name':site.sitename.replace('"','').encode('ascii','replace'),
'totpop':int(site.totpop)}
if site.values:
for n,v in enumerate(site.values):
#print v,type(v)
dicin['values%s'%n] = str(v)
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
t = self.g.simstep
dicin['incidence']= str(site.incidence[t])
dicin['arrivals'] = str(site.thetahist[t])
dicin['time'] = t
for n,v in enumerate(site.vnames):
#print i[n],type( i[n])
dicin[v] = str(i[n])
DO.Site(**dicin)
DO.Site._connection.commit()
#inserting data in edges table
for e in self.g.edge_list:
edicin={
'source_code':e.source.geocode,
'dest_code':e.dest.geocode}
edicin['time'] = t
edicin['ftheta'] = e.ftheta[t]
edicin['btheta'] = e.btheta[t]
DO.Edge(**edicin)
DO.Edge._connection.commit()
sys.exit("commit successful")
def writeMetaTable(self, table):
"""
Creates a Meta-Info Table on the database with the contents of the .epg file
"""
try:
table = table+'_meta'
if self.backend.lower() == "mysql":
con = MySQLdb.connect(host=self.host, port=self.port,
user=self.usr,passwd=self.passw, db=self.db)
elif self.backend.lower() == "sqlite":
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
con = sqlite3.connect("Epigrass.sqlite")
os.chdir(self.dir)
# Create table
sqlstr1 = "CREATE TABLE %s("%table
vars = []
cfgitems = self.config.items()
for k, v in cfgitems:
vars.append(k.strip().replace(' ','_').replace('.', '$'))
sqlstr2 = ', '.join(["%s text"%i for i in vars])
Cursor = con.cursor()
Cursor.execute(sqlstr1+sqlstr2+');')
#doing inserts
values = [v.split('#')[0] for k, v in cfgitems]
# for k, v in cfgitems:
# v = v.split('#')[0]
# if not v:
# v = ' '
# values.append()
str3 = ','.join(['"%s"'%i for i in values])+')'
sqlstr3 = '''INSERT INTO %s VALUES(%s''' % (table, str3)
#print sqlstr3
Cursor.execute(sqlstr3)
finally:
if con:
con.commit()
con.close()
def outToDb(self,table):
"""
Insert simulation results on a mysql or SQLite table
"""
if self.backend.lower() == "mysql":
self.Say('Saving data on MySQL...')
elif self.backend.lower() == "sqlite":
self.Say('Saving data on SQLite...')
con=None
try:
table = table+'_'+self.now
self.writeMetaTable(table)
self.outtable = table
if self.backend.lower() == "mysql":
con = MySQLdb.connect(host=self.host, port=self.port,
user=self.usr,passwd=self.passw, db=self.db)
elif self.backend.lower() == "sqlite":
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
con = sqlite3.connect("Epigrass.sqlite")
os.chdir(self.dir)
# Define number of variables to be stored
nvar = len(self.g.site_list[0].ts[-1]) +4 #state variables, plus coords, plus incidence, plus infected arrivals.
str1 = '`%s` FLOAT(9),'*nvar #nvar variables in the table
str1lite = '%s REAL,'*nvar #nvar variables in the SQLite table
varnames = ['lat','longit']+list(self.g.site_list[0].vnames)+['incidence']+['Arrivals']
# print nvar, varnames, str1
str1 = str1[:len(str1)-1] % tuple(varnames) #insert variable names (MySQL)
str1lite = str1lite[:len(str1lite)-1] % tuple(varnames) #insert variable names (SQLITE)
Cursor = con.cursor()
str2 = """CREATE TABLE %s(
`geocode` INT( 9 ) ,
`time` INT( 9 ) ,
`name` varchar(128) ,
""" % table
str2lite = """CREATE TABLE %s(
geocode INTEGER ,
time INTEGER ,
name TEXT ,
""" % table
sql = str2+str1+');'
sqlite = str2lite+str1lite+');'
if self.backend.lower() == "mysql":
Cursor.execute(sql)
str3 = (nvar+3)*'%s,'
str3 = str3[:-1]+')'
elif self.backend.lower() == "sqlite":
Cursor.execute(sqlite)
str3 = (nvar+3)*'?,'
str3 = str3[:-1]+')'
sql2 = 'INSERT INTO %s' % table + ' VALUES('+str3
nvalues = []
for site in self.g.site_list:
geoc = site.geocode
lat = site.pos[0]
long = site.pos[1]
name = site.sitename
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
inc = site.incidence
thist = site.thetahist
t = 0
for i in ts:
tstep = str(t)
nvalues.append(tuple([geoc,tstep,name]+[lat,long]+list(i)+[inc[t]]+[float(thist[t])]))
t += 1
Cursor.executemany(sql2,nvalues)
#Creating a table for edge data
self.etable = etable = table+'e'
esql = """CREATE TABLE %s(
`source_code` INT( 9 ) ,
`dest_code` INT( 9 ) ,
`time` INT( 9 ) ,
`ftheta` FLOAT(9) ,
`btheta` FLOAT(9) );"""%etable
esqlite = """CREATE TABLE %s(
source_code INTEGER ,
dest_code INTEGER ,
time INTEGER ,
ftheta REAL ,
btheta REAL );"""%etable
if self.backend.lower() == "mysql":
Cursor.execute(esql)
esql2 = 'INSERT INTO %s' % etable + ' VALUES(%s,%s,%s,%s,%s)'
elif self.backend.lower() == "sqlite":
Cursor.execute(esqlite)
esql2 = 'INSERT INTO %s' % etable + ' VALUES(?,?,?,?,?)'
values = []
for e in self.g.edge_list:
s = e.source.geocode
d = e.dest.geocode
t=0
for f,b in zip(e.ftheta,e.btheta):
values.append((s,d,t,f,b))
t += 1
Cursor.executemany(esql2,values)
finally:
if con:
con.close()
#saving pickle of adjacency matrix
matname = 'adj_'+self.modelName # table
fname = os.path.join(self.outdir,matname)
adjfile = open(fname,'w')
cPickle.dump(self.g.getConnMatrix(),adjfile)
adjfile.close()
def criaAdjMatrix(self):
# saving the adjacency matrix
codeslist = [str(i.geocode) for i in self.g.site_list]
if not os.path.exists('adjmat.csv'):
self.Say('Saving the adjacency matrix...')
am = self.g.getConnMatrix()
amf = open ('adjmat.csv','w')
amf.write(','.join(codeslist)+'\n')
for row in am:
row = [str(i) for i in row]
amf.write(','.join(row)+'\n')
amf.close()
self.Say('Done!')
def dumpData(self):
"""
Dumps data as csv (comma-separated-values)
"""
## pid = os.fork()
## if pid:
## return
## else:
self.Say("Starting simulation Analysis")
curdir = os.getcwd()
if not self.outdir == curdir:
os.chdir(self.outdir)
codeslist = [str(i.geocode) for i in self.g.site_list]
self.criaAdjMatrix()
#saving the shortest path matrices
# if not os.path.exists('spmat.csv'):
# self.Say('Calculating the shortest path matrices...')
# ap = self.g.getAllPairs()
# f = open('ap','w')
# cPickle.dump(ap,f)
# f.close()
# spd = self.g.shortDistMatrix
# apf = open ('spmat.csv','w')
# apf.write(','.join(codeslist)+'\n')
# spdf = open ('spdmat.csv','w')
# spdf.write(','.join(codeslist)+'\n')
# for row in ap:
# row = [str(i) for i in row]
# apf.write(','.join(row)+'\n')
# apf.close()
# for row in spd:
# row = [str(i) for i in row]
# spdf.write(','.join(row)+'\n')
# spdf.close()
# print 'Done!'
#Saving epidemic path
self.Say('Saving Epidemic path...')
if self.round:
epp = codecs.open('epipath%s.csv'%str(self.round),'w',self.encoding)
else:
epp = codecs.open('epipath.csv','w',self.encoding)
epp.write('time,site,infector\n')
for i in self.g.epipath:
#print i
infectors = i[-1]
# sorting infectors by number of infective contributed
if len(infectors):
reverse_infectors = [ [v[1],v[0]] for v in infectors.items()]
reverse_infectors.sort()
mli = [reverse_infectors[j][1] for j in xrange(0,len(reverse_infectors))][-1].sitename#Most likely infector
else:
mli = 'NA'
#print i[1].sitename, type(i[1].sitename), mli
epp.write(str(i[0])+','+i[1].sitename+','+mli+'\n')
epp.close()
self.Say('Done!')
#saving Epistats
self.Say('Saving Epidemiological results...')
stats = [str(i) for i in self.g.getEpistats()]
seed = [s for s in self.g.site_list if s.geocode == self.seed[0][0]][0]
stats.pop(1) #Remove epispeed which is a vector
if os.path.exists('epistats.csv'):
stf = codecs.open('epistats.csv','a',self.encoding)#append to file
else:
stf = codecs.open('epistats.csv','w',self.encoding)#create a new file
stf.write('seed,name,size,infected_sites,spreadtime,median_survival,totvaccinated,totquarantined,seeddeg,seedpop\n')
## stf.write('seed,name,size,infected_sites,spreadtime,median_survival,totvaccinated,totquarantined,seeddeg,seedpop\n')
#scent = str(seed.getCentrality())
#sbetw = str(seed.getBetweeness())
#sthidx = str(seed.getThetaindex())
sdeg = str(seed.getDegree())
spop = str(seed.totpop)
sname =seed.sitename
sstats = '%s,%s'%(sdeg,spop)
# sstats = '%s,%s,%s,%s,%s'%(scent,sbetw,sthidx,sdeg,spop)
stf.write(str(self.seed[0][0])+','+sname+','+','.join(stats)+','+sstats+'\n')
stf.close()
self.Say('Done!')
#Saving site stats
self.Say('Saving site statistics...')
#self.g.getAllPairs()
if os.path.exists('sitestats.csv'):
sitef = codecs.open('sitestats.csv','a',self.encoding) #append to file
else:
sitef = codecs.open('sitestats.csv','w',self.encoding)
#sitef.write('round,geocode,name,infection_time,degree,centrality,betweeness,theta_index,distance,seed,seedname\n')
sitef.write('round,geocode,name,infection_time,degree,seed,seedname\n')
for s in self.g.site_list:
degree = str(s.getDegree())
#central = str(s.getCentrality())
#bet = str(s.getBetweeness())
#thidx = str(s.getThetaindex())
seedgc = str(self.seed[0][0])
seedname = seed.sitename
# f = open('ap','r')
# ap = cPickle.load(f)
# f.close()
# distseed = str(ap[codeslist.index(str(s.geocode)),codeslist.index(str(self.seed[0][0]))])
it = str(s.infected) #infection time
if it == 'FALSE':
it = 'NA'
# sitef.write(str(self.round)+','+str(s.geocode)+','+s.sitename+','+it+','+degree+','+central+','+bet+','+thidx+','+distseed+','+seedgc+','+seedname+'\n')
sitef.write(str(self.round)+','+str(s.geocode)+','+s.sitename+','+it+','+degree+','+seedgc+','+seedname+'\n')
os.chdir(curdir)
self.Say('Done saving data!')
def saveModel(self,fname):
"""
Save the fully specified graph.
"""
f = open(fname,'w')
cPickle.dump(self.g,f)
f.close()
def loadModel(self,fname):
"""
Loads a pre-saved graph.
"""
g = cPickle.load(fname)
return g
def fins(self):
"""
call parallel inserts
"""
def runGraph(self,graphobj,iterations=1, transp=0):
"""
Starts the simulation on a graph.
"""
g = graphobj
g.maxstep = iterations
sites = tuple(graphobj.site_list)
edges = tuple(graphobj.edge_list)
#viewer = Viewer(g,self.shapefile[0], "geocode" )
if transp:
for n in xrange(iterations):
for i in sites:
i.runModel()
for j in edges:
j.transportStoD()
j.transportDtoS()
## self.outToODb(self.modelName,mode='p')
if self.gui:
# self.gui.graphDisplay.drawStep(g.simstep, dict([(s.geocode, s.incidence[-1]) for s in sites]))
self.gui.stepLCD.display(g.simstep)
self.gui.app.processEvents()
# self.gui.RT.mutex.lock()
# self.gui.RT.emit(self.gui.QtCore.SIGNAL("drawStep"), g.simstep, dict([(s.geocode, s.incidence[-1]) for s in sites]))
# self.gui.RT.mutex.unlock()
g.simstep += 1
else:
for n in xrange(iterations):
for i in sites:
i.runModel()
## self.outToODb(self.modelName,mode='p')
#viewer.show(n)
if self.gui:
#self.gui.graphDisplay.drawStep(g.simstep, dict([(s.geocode, s.incidence[-1]) for s in sites]))
self.gui.stepLCD.display(g.simstep)
self.gui.app.processEvents()
self.gui.RT.mutex.lock()
self.gui.RT.emit(self.gui.QtCore.SIGNAL("drawStep"), g.simstep, dict([(s.geocode, s.incidence[-1]) for s in sites]))
self.gui.RT.mutex.unlock()
g.simstep += 1
def Say(self,string):
"""
Exits outputs messages to the console or the gui accordingly
"""
if self.gui:
self.gui.textEdit1.insertPlainText(string+'\n''')
print string+'\n'
def storeSimulation(s,db='epigrass', host='localhost',port=3306):
"""
store the Simulate object *s* in the epigrass database
to allow distributed runs. Currently not working.
"""
now = time.asctime().replace(' ','_').replace(':','')
table = 'Model_'+S.modelName+now
con = MySQLdb.connect(host=host, port=port, user=usr,passwd=passw, db=db)
Cursor = con.cursor()
sql = """CREATE TABLE %s(
`simulation` BLOB);""" % table
Cursor.execute(sql)
blob = cPickle.dumps(s)
sql2 = 'INSERT INTO %s' % table + ' VALUES(%s)'
Cursor.execute(sql2,blob)
con.close()
class Bunch:
"""
Class to store a bunch os variables
"""
def __init__(self, **kw):
self.__dict__.update(kw)
class Tree:
"""
Tree object representing the spread of an epidemic
"""
def __init__(self,Simulation):
self.g = Simulation.g
Self.S = Simulation
pass
def writeNexus(self):
"""
Writes a Nexus file containing(.nex) the phylogeographical
tree of the epidemic.
"""
ntax = len(self.g.epipath)
sitenames = [i[1].sitename for i in self.g.epipath]
Name = self.S.modelName
header = """#NEXUS
[written %s from model % by EpiGrass]
"""%(time.asctime(),Name)
taxablock = """BEGIN TAXA;
TITLE %s;
DIMENSIONS NTAX=%s;
TAXLABELS
%s
;
END;
"""%(Name,ntax,' '.join(sitenames))
treeblock = """BEGIN TREES;
Title Epidemic_Path;
LINK Taxa = %s;"""%(Name,)
transtring = ','.join(['%s %s'%(i,j) for i,j in zip(range(1,len(sitenames)+1),sitenames)])+';'
treeblock2 = """TRANSLATE
%s
"""%transtring
venn = self.getVenn()
treeblock3 = """TREE 'Default ladder+' = %;
END;"""%venn
def getVenn(self):
""""
Generates Venn Diagram from epipath.
"""
pass
def onStraightRun(options, args):
"""
Runs the model from the commandline
"""
if options.backend =="mysql":
S = simulate(fname=args[0],host=options.dbhost, user=options.dbuser, password=options.dbpass, backend=options.backend)
else:
S = simulate(fname=args[0],backend=options.backend)
if not S.replicas:
S.start()
spread.Spread(S.g)
else:
repRuns(S)
if S.Batch:
self.Say('Simulation Started.')
# run the batch list
for i in S.Batch:
#Makes sure it comes back to original directory before opening models in the batch list
os.chdir(S.dir)
#delete the old graph object to save memory
S.graph = None
# Generates the simulation object
T = simulate(fname=i,host=S.host, user=S.usr, password=S.passw, backend=S.backend)
self.Say('starting model %s'%i)
T.start() # Start the simulation
# spread.Spread(T.g)
def repRuns(S):
"""
Do repeated runs
"""
randseed=S.randomize_seeds
fname=S.fname
host=S.host
user=S.usr
password=S.passw
backend=S.backend
nseeds= S.seed[0][2] #number o individual to be used as seeds
self.Say("Replication type: ", randseed)
if randseed:
seeds = S.randomizeSeed(randseed)
reps = S.replicas
for i in xrange(reps):
self.Say("Starting replicate number %s"%i)
S = simulate(fname=fname,host=host, user=user, password=password, backend=backend)
if randseed:
S.setSeed(seeds[i],nseeds)
S.round = i
S.shpout = False
S.start()
del S
def main():
# Options and Argument parsing for running model from the command line, without the GUI.
usage = "usage: %prog [options] your_model.epg"
parser = OptionParser(usage=usage, version="%prog "+__version__.version)
parser.add_option("-b", "--backend",type="string", dest="backend",
help="Define which datastorage backend to use", metavar="<mysql|sqlite|csv>", default="sqlite")
parser.add_option("-u", "--dbusername", type="string",
dest="dbuser", help="MySQL user name")
parser.add_option("-p", "--password", type="string",
dest="dbpass", help="MySQL password for user")
parser.add_option("-H", "--dbhost", type="string",
dest="dbhost",default="localhost", help="MySQL hostname or IP address")
(options, args) = parser.parse_args()
if options.backend == "mysql" and not (options.dbuser and options.dbpass):
parser.error("You must specify a user and password when using MySQL.")
if options.backend not in ['mysql', 'sqlite', 'csv']:
parser.error('"%s" is an invalid backend type.'%options.backend)
if args:
if len(args)<1:
parser.error("You must provide an EPG file to run.")
elif len(args)<1:
parser.error("Only a single EPG file can be specified.")
else:
if not os.path.exists(args[0]):
parser.error("The file '%s' does not exist."%args[0])
else:
parser.error("Wrong number of arguments.")
onStraightRun(options, args)
if __name__ == '__main__':
main()
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